CholesterolVolume 2011 (2011), Article ID 781643, 15 pagesdoi:10.1155/2011/781643

Review Article

Comparative Structures and Evolution of Vertebrate Carboxyl Ester Lipase (CEL) Genes and Proteins with a Major Role in Reverse Cholesterol Transport

Roger S. Holmes1,2,3 and Laura A. Cox1,2

¹Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78245-0549, USA²Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78245-0549, USA³School of Biomolecular and Physical Sciences, Griffith University, Nathan, QLD 4111, Australia

Received 25 June 2011; Accepted 30 August 2011

Academic Editor: Akihiro Inazu

Copyright © 2011 Roger S. Holmes and Laura A. Cox. Roger S. Holmes and . This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract.

Bile-salt activated carboxylic ester lipase (CEL) is a major triglyceride, cholesterol ester and vitamin ester hydrolytic enzyme contained within pancreatic and lactating mammary gland secretions. Bioinformatic methods were used to predict the amino acid sequences, secondary and tertiary structures and gene locations for CEL genes, and encoded proteins using data from several vertebrate genome projects. A proline-rich and O-glycosylated 11-amino acid C-terminal repeat sequence (VNTR) previously reported for human and other higher primate CEL proteins was also observed for other eutherian mammalian CEL sequences examined. In contrast, opossum CEL contained a single C-terminal copy of this sequence whereas CEL proteins from platypus, chicken, lizard, frog and several fish species lacked the VNTR sequence. Vertebrate CEL genes contained 11 coding exons. Evidence is presented for tandem duplicated CEL genes for the zebrafish genome. Vertebrate CEL protein subunits shared 53–97% sequence identities; demonstrated sequence alignments and identities for key CEL amino acid residues; and conservation of predicted secondary and tertiary structures with those previously reported for human CEL. Phylogenetic analyses demonstrated the relationships and potential evolutionary origins of the vertebrate CEL family of genes which were related to a nematode carboxylesterase (CES) gene and five mammalian CES gene families.

1. Introduction

Bile-salt activated carboxylic ester lipase (CEL; also designated as cholesterol esterase and lysophospholipase) is a major triglyceride, cholesterol ester and vitamin ester hydrolytic enzyme contained within pancreatic and lactating mammary gland secretions [5–10]. CEL is also secreted by the liver and is localized in plasma where it contributes to chylomicron assembly and secretion, the selective uptake of cholesteryl esters in HDL by the liver, LDL lipid metabolism, and reverse cholesterol transport [11–14]. Plasma CEL may also contribute to endothelial cell proliferation, the induction of vascular smooth muscle proliferation, and thrombus formation through interaction with platelet CXCR4 [15]. More recently, CEL expression has been reported in human pituitary glands where it may function in regulating hormone secretion in association with the CEL hydrolytic activity of ceramides [16].

Structures for several human and animal CEL genes and cDNA sequences have been determined, including human (Homo sapiens) [7, 17–19], gorilla (Gorilla gorilla) [20], mouse (Mus musculus) [21–23], rat (Rattus norvegicus) [24–26], and cow (Bos taurus) CEL genes [1, 27]. The human CEL gene comprises 11 exons and is localized on chromosome 9 [28]. Several Alu repetitive sequence elements and putative transcription factor binding sites have been identified in the 5′-untranslated (UTR) region, including pancreatic-specific binding sites, which contribute to a high level of expression in the exocrine pancreas [17, 29, 30]. Exon 11 of the human CEL gene encodes a variable number of tandem repeat sequences region (VNTR) (17 repeats are most common) which is highly polymorphic in human populations and contributes to plasma cholesterol and lipid composition [13]. Moreover, rare CEL gene defects in this region are responsible for a monogenically derived diabetes condition called maturity-onset diabetes of the young type 8 (MODY8), also known as diabetes and pancreatic exocrine dysfunction (DPED), which causes a defect in insulin secretion [31, 32].

Human CEL is expressed predominantly in the lactating mammary gland and beta cells of the exocrine pancreas, where the enzyme contributes significantly to triglyceride, cholesterol ester and vitamin ester metabolism [5–10]. CEL also promotes large chylomicron production in the intestine, and its presence in plasma supports interactions with cholesterol and oxidized lipoproteins [11] which may influence atherosclerosis progression [12]. CEL expression has also been reported in the human pituitary gland, and a possible role for CEL in the regulation of hormone secretion and ceramide metabolism has been described [16]. Studies of Cel⁻/Cel⁻ knock out mice have shown that other enzymes besides CEL are predominantly responsible for the hydrolysis of dietary cholesteryl esters, retinyl esters, and triglycerides [33]. Metabolic studies of Cel-null mice however have reported that a lack of CEL activity causes an incomplete digestion of milk fat and lipid accumulation by enterocytes in the ileum of neonatal mice which suggests a major role for this enzyme in triglyceride hydrolysis in breast-fed animals [9, 34]. Moreover, reverse cholesterol transport is elevated in carboxyl ester lipase-knockout mice which supports a significant role for this enzyme in the biliary disposal of cholesterol from the body [14].

A CEL-like gene (designated as CELL) has also been identified on human and gorilla chromosome 9, about 10 kilobases downstream of CEL, which is transcribed in many tissues of the body but lacks exons 2–7 and is unlikely to be translated into protein [17, 20, 35]. The CELL pseudogene gene duplication apparently occurred prior to the separation of Hominidae (man, chimpanzee, gorilla, and orangutan) from Old World monkeys (macaque) with CELL being restricted to genomes of man and the great apes [20].

Three-dimensional structural analyses of human CEL have shown that the enzyme belongs to the alpha/beta hydrolase fold family with several key structural and catalytic features, including an active site catalytic triad located within the enzyme structure and partially covered by a surface loop, the carboxyl terminus region of the protein which regulates enzymatic activity by forming hydrogen bonds with the surface loop to partially shield the active site, and a loop domain which binds bile salt and frees the active site to access water-insoluble substrates [1, 10, 36–38]. In both conformations, CEL forms dimeric subunit structures with active sites facing each other. The common variant of the human CEL gene contains VNTR repeats, but there is a high degree of polymorphism in the repeated region [31, 32]. While the biological function of the polymorphic repeat region is unknown, it has been suggested that it may be important for protein stability and/or secretion of the enzyme, particularly given that this region contains many O-glycosyl bonds linking carbohydrate residues to the CEL C-terminus, including fucose, galactose, glucosamine, galactosamine, and neuraminic acid residues [39].

This paper reports the predicted gene structures and amino acid sequences for several vertebrate CEL genes and proteins, the predicted secondary and tertiary structures for vertebrate CEL protein subunits, and the structural phylogenetic and evolutionary relationships for these genes and enzymes with mammalian CES (carboxylesterase) gene families [40, 41].

2. Methods

2.1. Vertebrate CEL Gene and Protein Identification

BLAST (Basic Local Alignment Search Tool) studies were undertaken using web tools from the National Center for Biotechnology Information (NCBI) (http://blast.ncbi.nlm.nih.gov/Blast.cgi) [42]. Protein BLAST analyses used vertebrate CEL amino acid sequences previously described (Table 1). Nonredundant protein sequence databases for several mammalian genomes were examined using the blastp algorithm, including human (Homo sapiens) [43], chimp (Pan troglodytes) [44], orangutan (Pongo abelii) (http://genome.wustl.edu/); the cow (Bos Taurus) [45], horse (Equus caballus) [46], mouse (Mus musculus) [47], opossum (Monodelphis domestica) [48], platypus [49], chicken (Gallus gallus) [50], clawed toad (Xenopus tropicalis) [51], and zebrafish (Danio rerio) [52]. This procedure produced multiple BLAST “hits” for each of the protein databases which were individually examined and retained in FASTA format, and a record kept of the sequences for predicted mRNAs and encoded CEL-like proteins. These records were derived from annotated genomic sequences using the gene prediction method: GNOMON and predicted sequences with high similarity scores for human CEL [42]. Predicted CEL-like protein sequences were obtained in each case and subjected to analyses of predicted protein and gene structures.

Table 1: Vertebrate CEL, human and mouse carboxylesterase (CES1–5) and nematode CES genes and subunits.

Vertebrate
Species
Gene CEL
RefSeq ID Prediction1,2
GenBank ID
Chromosome location
Exons (strand)
Gene size (bps)
UNIPROT ID
Amino acids
Subunit MW
pI
No. of repeats

Human
Homo Sapiens
CEL
NM_001807
BC042510
9:134, 927, 202-134, 936, 969
11 (+ve)
9,768
P19835
756
79,667
5.1
17

Gorilla
Gorilla gorilla
CEL
sc⁴6591²
³
sc6591⁴:90, 194-97, 985
³
7,791
Q9N1D1
998
101,026
4.5
39

Rhesus
Macaca mulatta
CEL
chr15.6.020²
³
15:5, 562, 165-5, 571, 662
11 (−ve)
9,498
³
731
78,302
4.8
15

Mouse
Mus musculus
CEL
NM_009885
BC006872
2:28, 411, 584-28, 418, 882
11 (−ve)
7,543
Q64285
598
65,666
5.9
3

Rat
Rattus norvegicus
CEL
NM_016997
M15893
3:7, 541, 329-7, 549, 228
11 (−ve)
7,900
P07882
612
67,052
5.3
4

Guinea pig
Cavia porcellus
CEL
sc⁴27.013.1²
³
sc27⁴:846, 072-851, 868
11 (−ve)
5,797
³
598
65,174
5.4
3

Cow
Bos taurus
CEL
NP_001013601
BC149530
11:106, 810, 242-106, 819, 101
11 (+ve)
8,762
P30122
599
65,598
5.2
3

Horse
Equus caballus
CEL
chr25.415.1²
³
25:35, 342, 417-35, 350, 330
11 (+ve)
7,914
³
599
65,310
5.3
3

Dog
Canis familiaris
CEL
chr9.55.011²
³
9:54, 678, 403-54, 686, 294
11 (−ve)
7,892
³
709
75,920
5.4
13

Opossum
Monodelphis domestica
CEL
chr1.10.178²
³
1:460, 155, 249-460, 171, 513
11 (+ve)
16,265
³
579
63,553
6.4
1

Platypus
Ornithorhynchus anatinus
CEL
ENSOANT23206²
³
Ultra81⁴:471, 532-485, 254
11 (+ve)
13,723
³
557
61,672
7.1
0

Chicken
Gallus gallus
CEL
NP_001013015¹
BX950478
17:7, 428, 231-7, 433, 490
11 (+ve)
5,260
³
556
61,191
6.6
0

Lizard
Anolis carolinensis
CEL
ENSACAT4924²
³
353⁴:801, 542-811, 604
11 (+ve)
10,063
³
553
61,438
6.1
0

Frog
Xenopus tropicalis
CEL
NP_001120027¹
³
191⁴:155, 996-171, 454
11 (−ve)
15,459
³
552
60,653
6.2
0

Zebrafish
Danio rerio
CEL1
NM_199607
BC079529
21:4, 281, 250-4, 291, 233
11 (−ve)
9,984
³
550
60,521
6.0
0

Zebrafish
Danio rerio
CEL2
AAH65887⁵
BC096893
21:4, 298, 674-4, 307, 810
11 (−ve)
9,137
³
550
60,425
6.1
0

Stickleback
Gasterosteus aculeatus
CEL
ENSGACT24004²
³
XIV:11, 357, 393-11, 361, 602
11 (−ve)
4,210
³
555
60,963
5.7
0

Medaka
Oryzias latipes
CEL
ENSORLT18090²
³
12:26, 977, 209-26, 983, 642
11 (+ve)
6,434
³
552
60,329
5.8
0

Fugu
Takifugu rubripes
CEL
ENSTRUG2423²
³
sc370⁴:307, 466, 106-307, 469, 087
11 (−ve)
2,982
³
554
61,498
6.7
0

Pufferfish
Tetraodon nigroviridis
CEL
CAF94246
CR654166
Un⁵:12, 727, 719-12, 730, 519
11 (−ve)
4,210
³
555
60,859
5.7
0

CES

Human
Homo Sapiens
CES1
NM_001025195
L07765
16:54, 394, 465-54, 424, 468
14 (−ve)
30,004
P23141
567
62,521
6.2
³

Mouse
Mus musculus
CES1a
NM_001013764
BC089371
8:95, 544, 116-95, 572, 091
14 (−ve)
27,979
Q5FWH4
563
61,744
5.1
³

Human
Homo Sapiens
CES2
NM_003869
BC032095
16:65, 527, 040-65, 535, 426
12 (+ve)
8,387
O00748
559
61,807
5.7
³

Mouse
Mus musculus
Ces2a
NM_133960
BC024491
8:107, 257, 972-107, 265, 313
12 (+ve)
7,342
Q8QZR3
558
61,940
5.7
³

Human
Homo Sapiens
CES3
NM_024922
BC053670
16:65, 552, 712-65, 564, 450
13 (+ve)
11,739
Q9H6X7
571
62,282
5.4
³

Mouse
Mus musculus
Ces3a
NM_198672
AK138932
8:107, 572, 572-107, 582, 000
13 (+ve)
21,512
Q63880
554
61,510
5.8
³

Human
Homo Sapiens
CES4A
NM_173815
BC166638
16:65, 580, 177-65, 600, 543
14 (+ve)
20,367
Q5XG92
561
60,366
9.4
³

Mouse
Mus musculus
Ces4a
NM_146213
BC026374
8:107, 655, 852-107, 673, 417
14 (+ve)
17,566
³
563
62,123
8.8
³

Human
Homo Sapiens
CES5A
NM_001143685
BC039073
16:54, 437, 867-54, 466, 634
13 (−ve)
27,768
Q6NT32
575
63,936
6.0
³

Mouse
Mus musculus
Ces5a
NM_001003951
AB186393
8:96, 038, 095-96, 059, 607
13 (+ve)
21,512
Q8R0W5
575
64,167
5.5
³

Nematode
Caenorhabditis elegans
T28C12
NM_072212
AAB66159
V:6, 323, 188-6, 326, 373
9 (+ve)
3,186
Q4LDP0
658
74,736
9.2
³

RefSeq refers to the NCBI reference sequence; ¹predicted NCBI sequence; ²predicted UCSC Genome Browser sequence; ³not available; ⁴gene scaffold ID; ⁵unidentified chromosome; pI refers to isoelectric point; bps refers to base pairs of nucleotide sequence; repeats number refers to the number of VNTR sequences at the CEL C-terminus.

BLAT (BLAST-Like Alignment Tool) analyses were subsequently undertaken for each of the predicted vertebrate CEL amino acid sequences using the University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/cgi-bin/hgBlat) [4] with the default settings to obtain the predicted locations for each of the vertebrate CEL genes, including predicted exon boundary locations and gene sizes. Structures for human, mouse, and rat CEL isoforms (splice variants) were obtained using the AceView website (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?human) to examine predicted gene and protein structures [2]. Alignments of vertebrate CEL sequences with human carboxylesterase (CES) protein sequences were assembled using the ClustalW2 multiple sequence alignment program [53] (http://www.ebi.ac.uk/Tools/clustalw2/index.html).

2.2. Predicted Structures and Properties of Vertebrate CEL Protein Subunits

Predicted secondary and tertiary structures for vertebrate CEL-like subunits were obtained using the PSIPRED v2.5 web site tools (http://bioinf.cs.ucl.ac.uk/psipred/) [54] and the SWISS MODEL web tools (http://swissmodel.expasy.org/), respectively [55, 56]. The reported tertiary structure for bovine CEL (PDB: 1aqlB) [1] served as the reference for the predicted human and zebrafish CEL tertiary structures, with a modeling range of residues 21 to 552. Theoretical isoelectric points and molecular weights for vertebrate CEL subunits were obtained using Expasy web tools (http://au.expasy.org/tools/pi_tool.html). SignalP 3.0 web tools were used to predict the presence and location of signal peptide cleavage sites (http://www.cbs.dtu.dk/services/SignalP/) for each of the predicted vertebrate CEL sequences [57]. The NetNGlyc 1.0 Server was used to predict potential N-glycosylation sites for vertebrate CEL subunits (http://www.cbs.dtu.dk/services/NetNGlyc/).

2.3. Comparative Human (CEL) and Mouse (Cel) Tissue Expression

The UCSC Genome Browser (http://genome.ucsc.edu/) [4] was used to examine GNF1 Expression Atlas 2 data using various expression chips for human CEL and mouse Cel genes, respectively, (http://biogps.gnf.org/) [3]. Gene array expression “heat maps” were examined for comparative gene expression levels among human and mouse tissues showing high (red), intermediate (black), and low (green) expression levels.

2.4. Phylogenetic Studies and Sequence Divergence

Alignments of vertebrate CEL and human, mouse, and nematode CES-like (carboxylesterase) protein sequences were assembled using BioEdit v.5.0.1 and the default settings [58]. Alignment ambiguous regions were excluded prior to phylogenetic analysis yielding alignments of 480 residues for comparisons of sequences (Table 1). Evolutionary distances were calculated using the Kimura option [59] in TREECON [60]. Phylogenetic trees were constructed from evolutionary distances using the neighbor-joining method [61] and rooted with the nematode CES sequence. Tree topology was reexamined by the boot-strap method (100 bootstraps were applied) of resampling, and only values that were highly significant (≥90) are shown [62].

3. Results and Discussion

3.1. Alignments of Human and Other Vertebrate CEL Subunits

The deduced amino acid sequences for opossum (Monodelphis domestica) and chicken (Gallus gallus) CEL subunits and for zebrafish (Danio rerio) CEL1 and CEL2 subunits are shown in Figure 1 together with the previously reported sequences for human (Homo sapiens) [7, 39], mouse (Mus musculus) [22], and bovine (Bos taurus) [27, 63] CEL subunits (Table 1). Alignments of the human and other vertebrate CEL subunits examined in this figure showed between 56–80% sequence identities, suggesting that these are products of the same family of genes and proteins (Table 2). The amino acid sequence for human CEL contained 756 residues whereas other vertebrate CEL subunits contained fewer amino acids: 599 residues (cow), 598 residues (mouse), 579 residues (opossum), 556 residues (chicken), and 550 residues for zebrafish CEL1 and CEL2 (Figure 1; Table 1). These differences are predominantly explained by changes in the number of VNTR 11 residue repeats at the respective CEL C-termini, with human CEL containing 17 repeats, whereas bovine, mouse, and opossum CEL C-termini contained only 3, 3, and 1 repeats, respectively, while chicken and zebrafish CEL subunits exhibited no VNTR-like C-terminus sequences. Table 1 summarizes this feature among all of the vertebrate CEL sequences examined and shows that substantial numbers of C-terminus VNTR repeats were predominantly restricted to higher primates, especially gorilla (Gorilla gorilla) (39 repeats) [20], human (17 repeats) [17], and rhesus (Macaca mulatta) (15 repeats) CEL, whereas other mammalian CEL subunits usually contained 3 VNTR repeats, with the exception of the predicted dog (Canis familiaris) CELC-terminus, which contained 13 VNTR-repeat sequences. A comparison of the 11-residue repeat sequences for the mammalian CEL subunits examined showed the following consensus sequence: Pro-Val-Pro-Pro-Thr-Gly-Asp-Ser-Glu-Ala-Ala (Figure 2), for which the first 4 residues have been proposed to play a role in facilitating O-glycosylation at the 5th residue (Thr) position [10].

Table 2: Percentage identities for vertebrate CEL subunit amino acid sequences.

Vertebrate
Human
Chimp
Gorilla
Rhesus
Marmoset
Mouse
Rat
G pig
Cow
Horse
Dog
Opossum
Platypus
Chick
Frog
Zfish 1
Zfish 2
Pufferfish
Medaka
Fugu

Human
100
97
97
93
92
80
80
78
78
84
86
84
75
65
65
56
58
53
54
54

Chimp
97
100
97
93
91
80
80
78
79
84
86
83
75
65
65
56
58
53
54
54

Gorilla
97
97
100
93
93
80
80
78
79
84
86
83
75
65
65
56
58
54
55
54

Rhesus
93
93
93
100
92
80
80
79
80
85
87
84
76
65
66
57
58
55
55
55

Marmoset
92
91
93
92
100
81
82
79
80
85
87
85
76
66
67
57
59
53
56
54

Mouse
80
80
80
80
81
100
93
80
78
77
80
77
72
63
63
57
59
53
55
53

Rat
80
80
80
80
82
93
100
82
79
78
79
78
73
64
63
58
60
55
56
54

Guinea pig
78
78
78
79
79
80
82
100
78
79
78
77
73
64
65
57
59
54
56
55

Cow
78
79
79
80
80
78
79
78
100
81
81
78
73
66
65
57
58
56
57
56

Horse
84
84
84
85
85
77
78
79
81
100
85
81
75
67
65
58
59
55
56
55

Dog
86
86
86
87
87
80
79
78
81
85
100
83
77
66
64
58
59
54
55
55

Opossum
84
83
83
84
85
77
78
77
78
81
83
100
77
65
65
57
58
55
55
54

Platypus
75
75
75
76
76
72
73
73
73
75
77
77
100
66
62
55
57
54
54
55

Chick
65
65
65
65
66
63
64
64
66
67
66
65
66
100
67
60
62
56
58
56

Frog
65
65
65
66
67
63
63
65
65
65
64
65
62
67
100
58
57
57
58
56

Zfish 1
56
56
56
57
57
57
58
57
57
58
58
57
55
60
58
100
86
64
63
64

Zfish 2
58
58
58
58
59
59
60
59
58
59
59
58
57
62
57
86
100
62
66
63

Pufferfish
53
53
54
55
53
53
55
54
56
55
54
55
54
56
57
64
62
100
71
83

Medaka
54
54
55
55
56
55
56
56
57
56
55
55
54
58
58
63
66
71
100
72

Fugu
54
54
54
55
54
53
54
55
56
55
55
54
55
56
56
64
63
83
72
100

Zfish refers to zebrafish (Danio rerio) CEL; Gpig refers to guinea pig CEL (Cavia porcellus).

Figure 1: Amino acid sequence alignments for human and other vertebrate CEL subunits. See Table 1 for sources of CEL sequences; * shows identical residues for CEL subunits;: similar alternate residues;. dissimilar alternate residues; N-Signal peptide residues are in red; N-glycosylation residues at 207NIT (human CEL) are in green; active site (AS) triad residues Ser, Asp, and His are in pink; O-glycosylation sites are in blue; disulfide bond Cys residues for human CEL (•); essential arginines which contribute to bile-salt binding are in red; helix (human CEL or predicted helix); sheet (human CEL) or predicted sheet; bold font shows known or predicted exon junctions; exon numbers refer to human CEL gene; CEL “loop” covering the active site (human CEL residues 136–143) are in green; Hu-human CEL; Co-cow CEL; Mo-mouse CEL; Op-opossum CEL; Ch-chicken CEL; Z1-zebrafish CEL1; Z2-zebrafish CEL2.

Figure 2: Amino acid alignments for C-terminal 11-residue repeat sequences for mammalian CEL subunits. Hydrophobic amino acid residues are shown in red; hydrophilic residues in green; acidic residues in blue; basic residues in pink; (squared T) refers to known O-glycosylation sites for human CEL; R refers to repeat number. P-proline; V-valine; T-threonine; G-glycine; D-aspartate; E-glutamate; S-serine; A-alanine; K-lysine; N-asparagine; note consistent PVPP start sequences.

Several other key amino acid residues for mammalian CEL have been recognized (sequence numbers refer to human CEL) (Figure 1). These include the catalytic triad for the active site (Ser194; Asp320; His435) forming a charge relay network for substrate hydrolysis [10, 64]; the hydrophobic N-terminus signal peptide (residues 1–20) [7, 65]; disulfide bond forming residues (Cys84/Cys100 and Cys266/Cys277) [7, 66]; arginine residues (Arg83/Arg446) which contribute to bile-salt binding and activation [1, 36]; a heparin binding site (residues 21–121); as well as the 11-residue VNTR repeat (×17) at the CEL C-terminus (residues 562–756). Identical residues were observed for each of the vertebrate CEL subunits for the active site triad, disulfide bond forming residues and key arginine residues contributing to bile salt activation, however, the N-terminus 20-residue signal peptide underwent changes in sequence but retained predicted signal peptide properties (Figure 1; Table 1). The N-glycosylation site reported for human CEL at Asn207-Ile208-Thr209 [10] was retained for each of the 22 vertebrate CEL sequences examined, with the exception of platypus (Ornithorhynchus anatinus) CEL which contained two predicted N-glycosylation sites at Asn381-Val382-Thr383 and Asn548-Leu549-Thr550 (Table 3). Predicted N-glycosylation sites were also observed at other positions, including Asn381-Ile382-Thr383 for opossum (Monodelphis domestica) CEL; Asn270-Thr271-Thr272 and Asn381-Leu382-Thr383 for chicken (Gallus gallus) CEL; Asn270-Thr271-Thr272 for lizard (Anolis carolensis); Asn550-Val551-Thr552 for fugu (Takifugu rupides) CEL (Table 3). Given the reported role of the N-glycosylated carbohydrate group in contributing to the stability and maintaining catalytic efficiency of a related enzyme (carboxylesterase or CES1) [67], this property may be shared by the vertebrate CEL subunits as well, especially for those containing multiple predicted sites for N-glycosylation, such as chicken CEL, which contains three such sites.

Table 3: Known or predicted N-glycosylation sites for vertebrate CEL subunits.

Vertebrate
Site 1
Site 2
Site 3
Site 4
Site 5
Site 6
No of sites

CEL

Human
210NIT

1

Chimp
207NIT

1

Gorilla
210NIT

518NGS

1

Rhesus
207NLT

515NGS

1

Marmoset
207NIT

515NGS

1

Mouse
207NIT

325NNT

1

Rat
207NIT

1

Guinea pig
207NIT

1

Cow
207NIT

381NAT

1

Horse
207NIT

381NAT
515NSS

1

Dog
207NIT

381NST

567NAT
1

Opossum
207NIT

381NIT

2

Platypus

381NVT

548NLT
2

Chicken
207NIT
270NTT

381NLT

3

Lizard
207NIT
270NTT

2

Frog
207NIT

1

Zebrafish 1
204NIT

1

Zebrafish 2
204NIT

1

Pufferfish
204NIT

1

Fugu
204NIT

550NVT
2

Stickleback
205NIT

1

Medaka
204NIT

1

The identified N-glycosylation site is for human CEL (see [10]). Amino acid residues are shown for known or predicted N-glycosylation sites: N-Asn; A-Ala; T-Thr; S-Ser; M-Met; L-Leu; D-Asp; G-Gly; F-Phe; I-Ile; V-Val; sites with high probabilities for N-glycosylation are written in bold face.

3.2. Predicted Secondary and Tertiary Structures of Vertebrate CEL Subunits

Analyses of predicted secondary structures for vertebrate CEL sequences were compared with the previously reported secondary structure for bovine and human CEL [1, 68] (Figure 1). Similar α-helix β-sheet structures were observed for all of the vertebrate CEL subunits examined. Consistent structures were particularly apparent near key residues or functional domains including the β-sheet and α-helix structures near the active site Ser194 (β8/αD) and Asp320 (β10/α8) residues, and the N-glycosylation site at Asn207-Ile208-Thr209 (near β8) [69]. The single helix at the C-termini (αN) for the vertebrate CEL subunits was readily apparent, as were the five β-sheet structures at the N-termini of the CEL subunits (β1–β5). It is apparent from these studies that all of these CEL subunits have highly similar secondary structures.

Figure 3 describes predicted tertiary structures for mouse CEL and zebrafish CEL1 protein sequences which showed significant similarities for these polypeptides with bovine [1, 36] and human CEL [68]. Identification of specific structures within the predicted mouse CEL and zebrafish CEL1 sequences was based on the reported structure for a truncated human CEL which identifies a sequence of twisted β-sheets interspersed with several α-helical structures [10, 68] which are typical of the alpha-beta hydrolase superfamily [40]. The active site CEL triad was centrally located which is similar to that observed in other lipases and esterases [40, 70, 71]. The major difference between CEL and other serine esterases is an apparent insertion at positions 139–146 (for human CEL) (Figure  1 of Supplementary Material available online at doi 10.1155/2011/781643) which appears to act as a surface loop that partially covers the opening to the catalytic triad and allows access to the active site by water soluble substrates by the truncated CEL [68]. This active site loop is also readily apparent in the predicted structures for mouse CEL and zebrafish CEL1. These comparative studies of vertebrate CEL proteins suggest that the properties, structures, and key sequences are substantially retained for all of the vertebrate sequences examined.

Figure 3: Predicted tertiary structures for mouse CEL and zebrafish CEL1 subunits. The predicted mouse CEL and zebrafish CEL1 3-D structures were obtained using the SWISS MODEL web site http://swissmodel.expasy.org/ and based on the reported structure for bovine CEL (PDB: 1aqlB) [1]; the rainbow color code describes the 3-D structures from the N- (blue) to C-termini (red color); N refers to amino terminus; C refers to carboxyl terminus; specific alpha helices (αA … αN) and beta sheets (β1 … β13) were identified, as well as the active site region and the “loop” covering the active site.

3.3. Predicted Gene Locations and Exonic Structures for Vertebrate CEL Genes

Table 1 summarizes the predicted locations for vertebrate CEL genes based upon BLAT interrogations of several vertebrate genomes using the reported sequences for human, gorilla, mouse, rat, and bovine CEL [6, 7, 20, 22–24, 27] and the predicted sequences for other vertebrate CEL proteins and the UCSC Genome Browser [4]. Human and mouse CEL genes were located on human chromosome 9 and mouse chromosome 2, which are distinct to the carboxylesterase (CES for human or Ces for mouse) gene family cluster locations in each case: on human chromosome 16 and mouse chromosome 8, respectively (Table 1; see [41]). The zebrafish (Danio rerio) genome showed evidence of tandem duplicated CEL genes, with predicted CEL1 and CEL2 genes being located about 7.3 kilobases apart on zebrafish chromosome 21 (Table 1). This is in contrast with many other gene duplication events during zebrafish evolution that have occurred predominantly by polyploidisation or duplication of large chromosomal segments rather than by tandem gene duplication [72].

Figure 1 summarizes the predicted exonic start sites for cow, opossum, chicken, and zebrafish CEL genes with each having 11 exons, in identical or similar positions to those reported for the human CEL and mouse Cel genes [17, 22, 23]. In contrast, human CES1 [73, 74], CES2, CES3 [75, 76], CES4 [41], and CES5 [77, 78] genes contained 14, 12, 13, 14, and 13 exons, respectively, which are predominantly in distinct positions to those described for vertebrate CEL genes, with the exception of the last exon in each case (Figure  1 of Supplementary Material). Consequently, even though CEL and CES genes and proteins are members of the same serine hydrolase superfamily [10, 40], it is apparent that CEL is not a close relative of the CES gene family, for which at least five genes are clustered on a single chromosomes on human and mouse chromosomes and are more similar in gene structure to each other than they are to the CEL gene (Figure  1 of Supplementary Material; see [41]).

Figure 4 illustrates the predicted structures of mRNAs for human and mouse CEL transcripts for the major transcript isoform in each case [2]. The transcripts were 10.5 and 7.6 kilobases in length, respectively, with 10 introns and 11 exons present for these CEL mRNA transcripts. The human CEL genome sequence contained a microRNA site (miR485-5p) located in the 3′-untranslated region and a CpG island (CpG51). The occurrence of the CpG island within the CEL gene may reflect a role in regulating gene expression [79] which may contribute to a higher than average gene expression level reported for human CEL (×1.5 times higher). Figure  2 of Supplementary Material shows a nucleotide sequence alignment diagram for the CpG51 region of the human CEL gene in comparison with several other mammalian and other vertebrate CEL genes. The Multiz alignment patterns observed demonstrated extensive sequence conservation for the CpG island which contains dinucleotide and trinucleotide repeat sequences in most genomes examined.

Figure 4: Gene structures for the human and mouse CEL genes. Derived from AceView website http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/ [2]; the major isoform variant is shown with capped 5′- and 3′- ends for the predicted mRNA sequences; introns and exons are numbered; the length of the mRNAs (as kilobases or kb) and comparative expression levels with the average gene are shown; a CpG island (CpG51); several predicted transcription factor binding sites; and a MiRNA485-5p binding site were identified for the human CEL gene; the direction for transcription is shown; 3′UTR refers to 3′-untranslated region.

The prediction of a microRNA (miRNA; miR485-5p) binding site in the 3′untranslated region of human CEL is also potentially of major significance for the regulation of this gene. MicroRNAs are small noncoding RNAs that regulate mRNA and protein expression and have been implicated in regulating gene expression during embryonic development [80]. Moreover, a recent study of a related miRNA gene (miR-375) has been recently shown to be selectively expressed in pancreatic islets and has been implicated both in the development of islets and the function of mature pancreatic beta cells [81]. A similar role may be played by miR485-5p with respect to the regulation of CEL expression during pancreatic beta cell development. Table  1 of Supplementary Material presents comparative nucleotide sequences for miR485-5p-like CEL gene regions for several vertebrate genomes which shows high levels of sequence identity, particularly among mammalian CEL miRNA target sites and suggests that this site has been predominantly conserved during vertebrate evolution, particularly by eutherian mammalian CEL genes.

Figure 5 shows a UCSC Genome Browser Comparative Genomics track that shows evolutionary conservation and alignments of the nucleotide sequences for the human CEL gene, including the 5′-flanking, 5′-untranslated, intronic, exonic, and 3′untranslated regions of this gene, with the corresponding sequences for 10 vertebrate genomes, including 5 eutherian mammals (e.g., mouse, rat), a marsupial (opossum), a monotreme (platypus), and lower vertebrate genomes. Extensive conservation was observed among these genomic sequences, particularly for the rhesus CEL gene and for other eutherian mammalian genomes. In contrast with the eutherian mammalian genomes examined, other vertebrate genomes retained conserved sequences only within the 11 exonic CEL regions. It would appear that exonic CEL nucleotide sequences have been conserved throughout vertebrate evolution whereas only in eutherian mammalian genomes have other regions of the CEL gene been predominantly conserved.

Figure 5: Comparative sequences for vertebrate 5′-flanking, 5′-untranslated, and coding regions for the CEL genes. Derived from the UCSC Genome Browser using the Comparative Genomics track to examine alignments and evolutionary conservation of CEL gene sequences; genomic sequences aligned for this study included primate (human and rhesus), nonprimate eutherian mammal (mouse, dog and elephant), a marsupial (opossum), a monotreme (platypus), bird (chicken), reptile (lizard), amphibian (frog), and fish (stickleback); conservation measures were based on conserved sequences across all of these species in the alignments which included the 5′flanking, 5′-untranslated (5′UTR), exons, introns, and 3′ untranslated (3′UTR) regions for the CEL gene; regions of sequence identity are shaded in different colors for different species; exons 1–11 are shown which are regions of conservation.

3.4. Comparative Human and Mouse CEL Tissue Expression

Figure 6 presents “heat maps” showing comparative gene expression for various human and mouse tissues obtained from GNF Expression Atlas Data using the GNF1H (human) and GNF1M (mouse) chips (http://genome.ucsc.edu/; http://biogps.gnf.org/) [3]. These data supported a high level of tissue expression for human CEL, particularly for the pancreatic islets, the pituitary gland, and fetal liver, which is consistent with previous reports for these genes (see [10]). High levels of CEL gene expression have also been reported for the human mammary gland where CEL plays a major role in lipid digestion in breast milk by neonates [6]. The localization of CEL within the human pituitary gland is of major interest as this enzyme also hydrolyzes ceramides [8], which suggests a possible role in the regulation of hormone secretion in both normal and adenomatous pituitary cells [16]. A high level of expression of CEL in mouse tissues was also observed (×3.4 times average expression) (Figure 4), particularly for the pancreas, mammary gland, and spleen (Figure 5), where similar metabolic roles for this enzyme in cholesterol ester, retinyl ester, and triglyceride hydrolysis and metabolism have been described [10]. Recent metabolic studies using Cel⁻/Cel⁻ (knock-out) mice (or CELKO mice) have demonstrated that CEL is not an essential enzyme for these metabolic functions [82, 83], although CELKO neonatal mice exhibit an incomplete digestion of milk fat [9, 84], and in adult CELKO mice causes an elevation in reverse cholesterol transport (RCT) in adult animals [14]. The latter finding is potentially of major clinical significance for this enzyme, given that any increase in RCT and the associated increased biliary disposal of cholesterol may contribute to preventing atherosclerosis [85, 86].

Figure 6: Comparative tissue expression for human and mouse CEL genes. Expression “heat maps” (GNF Expression Atlas 2 data) (http://biogps.gnf.org/) [3] were examined for comparative gene expression levels among selected human (GNF1H) and mouse (GNF1M) tissues for CEL showing high (red), intermediate (black), and low (green) expression levels. The results were derived from the human and mouse genome browsers (http://genome.ucsc.edu/) [4].

3.5. Phylogeny and Divergence of Vertebrate CEL and Mammalian/Nematode CES Sequences

A phylogenetic tree (Figure 7) was calculated by the progressive alignment of human and other vertebrate CEL amino acid sequences with human and mouse CES1, CES2, CES3, CES4, and CES5 sequences. The phylogram was “rooted” with a nematode CES sequence and showed clustering of the CEL sequences which were distinct from the human and mouse CES families. In addition, the zebrafish CEL1 and CEL2 sequences showed clustering within the fish CEL sequences examined, which is consistent with these genes being products of a recent duplication event during teleost fish evolution. Overall, these data suggest that the vertebrate CEL gene arose from a gene duplication event of an ancestral CES-like gene, resulting in at least two separate lines of gene evolution for CES-like and CEL-like genes. This is supported by the comparative biochemical and genomic evidence for vertebrate CEL and CES-like genes and encoded proteins, which share several key features of protein and gene structure, including having similar alpha-beta hydrolase secondary and tertiary structures [10, 40, 41, 71, 78] (Figure  1 of Supplementary Material).

Figure 7: Phylogenetic tree of vertebrate CEL with human and mouse CES1, CES2, CES3, CES4, and CES5 amino acid sequences. The tree is labeled with the gene name and the name of the vertebrate. Note the major cluster for the vertebrate CEL sequences and the separation of these sequences from human and mouse CES1, CES2, CES3, CES4, and CES5 sequences. The tree is “rooted” with the CES sequence (T27C12) from a nematode (Caenorhabditis elegans). See Table 1 for details of sequences and gene locations. A genetic distance scale is shown (% amino acid substitutions). The number of times a clade (sequences common to a node or branch) occurred in the bootstrap replicates are shown. Only replicate values of 90 or more which are highly significant are shown with 100 bootstrap replicates performed in each case.

In conclusion, the results of the present study indicate that vertebrate CEL genes and encoded CEL enzymes represent a distinct alpha-beta hydrolase gene and enzyme family which share key conserved sequences and structures that have been reported for the human CES gene families. CEL is a major triglyceride, cholesterol ester and vitamin ester hydrolytic enzyme contained within exocrine pancreatic and lactating mammary gland secretions and is also localized in plasma where it contributes to chylomicron assembly and secretion, in the selective uptake of cholesteryl esters in HDL in the liver and in reverse cholesterol transport, including biliary disposal of cholesterol. Bioinformatic methods were used to predict the amino acid sequences, secondary and tertiary structures and gene locations for CEL genes, and encoded proteins using data from several vertebrate genome projects. A proline-rich and O-glycosylated 11-amino acid C-terminal repeat sequence (VNTR) previously reported for human and other higher primate CEL proteins was also observed for other eutherian mammalian CEL sequences examined. Opossum CEL, however, contained a single C-terminal copy of this sequence while CEL proteins from lower vertebrates lacked the VNTR sequence. Evidence is presented for tandem duplicated CEL genes for the zebrafish genome. Vertebrate CEL protein subunits shared 53–97% sequence identities and exhibited sequence alignments and identities for key CEL amino acid residues as well as extensive conservation of predicted secondary and tertiary structures with those previously reported for human CEL. Phylogenetic analyses demonstrated the relationships and potential evolutionary origins of the vertebrate CEL family of genes which were related to a nematode carboxylesterase (CES) gene and five mammalian CES gene families. These studies indicated that CEL genes have apparently appeared early in vertebrate evolution prior to the teleost fish common ancestor more than 500 million years ago [87].

Acknowledgments

This project was supported by NIH Grants P01 HL028972 and P51 RR013986. In addition, this investigation was conducted in facilities constructed with support from Research Facilities Improvement Program Grant nos. 1 C06 RR13556, 1 C06 RR15456, and 1 C06 RR017515. The authors gratefully acknowledge the assistance of Dr Bharet Patel of Griffith University Brisbane Australia with the phylogeny studies.

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